Season 1 focused on Earth.
Season 2 focuses on Earth as well as alien threats from outer space and time travel.
If they do make a Season 3 how can it top aliens from outer space and time travel? Simple, the Multiverse.
The Young Justice world is part of DC's 52 Earths. It's classified as Earth-16.
They could introduce parallel Earth's through magic, science or any of the Speedsters. Several magical entities can create interdimensional portals. They can go the route of Justice League: Crisis on Two Earths and use a device to travel between Earths. In a Justice League Unlimted two-part episode "Legends" Flash vibrated in a way that made him sync with another parallel universe.
Also, in a trailer from DC Universe Online (is that game good?) Braniac wanted to get Earth because it was the key to the Multiverse.
This could introduce characters such as the Crime Syndicate.
So what do you guys think? Cool idea or maybe too much? Focus of Season 3 or maybe just a small side-plot?